PDBsum entry: 1b9o

Calcium-binding protein

PDB id: 1b9o

Contents

Protein chain

123 a.a. *

Metals

_CA

Waters ×164

* Residue conservation analysis

PDB id:

1b9o

Name:

Calcium-binding protein

Title:

Human alpha-lactalbumin, low temperature form

Structure:

Protein (alpha-lactalbumin). Chain: a

Source:

Homo sapiens. Human. Organism_taxid: 9606

Resolution:

1.15Å R-factor: 0.119 R-free: 0.162

Authors:

K.Harata,Y.Abe,M.Muraki

Key ref:

K.Harata et al. (1999). Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method. J Mol Biol, 287, 347-358. PubMed id: 10080897 DOI: 10.1006/jmbi.1999.2598

Date:

14-Feb-99 Release date: 31-Mar-99

Protein chain

P00709  (LALBA_HUMAN) -  Alpha-lactalbumin

Seq: 142 a.a.

Struc: 123 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: cell-cell signaling (5 terms)
• Biochemical function: protein binding (3 terms)

DOI no: 10.1006/jmbi.1999.2598

J Mol Biol 287:347-358 (1999)

PubMed id: 10080897

Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method.

K.Harata, Y.Abe, M.Muraki.

ABSTRACT

The low temperature form of human alpha-lactalbumin (HAL) was crystallized from a 2H2O solution and its structure was refined to the R value of 0.119 at 1.15 A resolution by the full-matrix least-squares method. Average estimated standard deviations of atomic parameters for non-hydrogen atoms were 0.038 A for coordinates and 0.044 A2 for anisotropic temperature factors (Uij). The magnitude of equivalent isotropic temperature factors (Ueqv) was highly correlated with the distance from the molecular centroid and fitted to a quadratic equation as a function of atomic coordinates. The atomic thermal motion was rather isotropic in the core region and the anisotropy increased towards the molecular surface. The statistical analysis revealed the out-of-plane motion of main-chain oxygen atoms, indicating that peptide groups are in rotational vibration around a Calpha.Calpha axis. The TLS model, which describes the rigid-body motion in terms of translation, libration, and screw motions, was adopted for the evaluation of the molecular motion and the TLS parameters were determined by the least-squares fit to Uij. The reproduced Ueqvcal from the TLS parameters was in fair agreement with observed Ueqv, but differences were found in regions of residues, 5-22, 44-48, 70-75, and 121-123, where Ueqv was larger than Ueqvcal because of large local motions. To evaluate the internal motion of HAL, the contribution of the rigid-body motion was determined to be 42.4 % of Ueqv in magnitude, which was the highest estimation to satisfy the condition that the Uijint tensors of the internal motion have positive eigen values. The internal motion represented with atomic thermal ellipsoids clearly showed local motions different from those observed in chicken-type lysozymes which have a backbone structure very similar to HAL. The result indicates that the internal motion is closely related to biological function of proteins.

Selected figure(s)

Figure 4.
Figure 4. Plot of (a) Ueqv and (b) anisotropy factor of C a against the square of the distance from the molecular centroid. The correlation coefficient is 0.685 for Ueqv and 0.444 for the anisotropy factor.

Figure 5.
Figure 5. Plot of observed (continuous line) and calcu- lated (broken line) Ueqv values against the residue num- ber.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 347-358) copyright 1999.

Figures were selected by an automated process.